genedata = Ensembl.EnsemblGenes(assembly=assembly)
genes = Ensembl.ReverseGeneMapping(genedata)
genespluspromotor = Ensembl.ReverseGeneMapping(
genedata, tssPadding=UPSTREAM_PROMOTOR_DIST)
genepromotors = Ensembl.ReversePromotorMapping(
genedata,
upstreamPadding=UPSTREAM_PROMOTOR_DIST,
downstreamPadding=DOWNSTREAM_PROMOTOR_DIST)
exons = Ensembl.ReverseExonMapping(genedata)
transcriptionSites = Ensembl.TranscriptionSites(genedata)
# UCSC table browser - Expression & Regulation - CpG Islands
# Download all columns with exception of "bin"
cpgIslands = ExtendedBed(
os.path.expanduser("/mnt/50tb/publicdata/" + assembly +
"/CpGIslands/cpgislands.bed"))
# UCSC table browser - Mapping and Sequencing - Chromosome Bands
# Download all columns with exception of "gieStain"
gBanding = ExtendedBed(os.path.expanduser("/mnt/50tb/publicdata/" + assembly +
"/G-Banding/cytogenetic.map.bed"),
defaultkeys=["chrm", "start", "stop", "band"],
forcekeys=True)
chromosomeEnds = ChromosomeEnds(assembly)
TSS_TTS_Distance = 5000
TTS_TTS_Distance_Human = str(TSS_TTS_Distance / 1000) + "kb"
Small_TSS_TTS_Distance = 1000
Small_TTS_TTS_Distance_Human = str(Small_TSS_TTS_Distance / 1000) + "kb"
# load data
genedata = Ensembl.EnsemblGenes(assembly="hg18", annotation="ncbi36.1")
genes = Ensembl.ReverseGeneMapping(genedata)
exons = Ensembl.ReverseExonMapping(genedata)
transcriptionSites = Ensembl.TranscriptionSites(genedata)
cpgIslands = ExtendedBed(
os.path.expanduser(
"~/mount/publicdata/hg18/cpgislands/cpgislands-0-index.bed"))
affyannotation = NetAffxAnnotation()
paddedGenes = Ensembl.ReverseGeneMapping(genedata, tssPadding=TSS_TTS_Distance)
def isUpstream(distance, strand):
if strand == "+":
return 'Y' if distance >= 0 else 'N'
elif strand == "-":
return 'Y' if distance <= 0 else 'N'